Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility

Maitra, A and Sarkar, MC and Raheja, H and Biswas, NK and Chakraborti, S and Singh, AK and Ghosh, S and Sarkar, S and Patra, S and Mondal, RK and Ghosh, T and Chatterjee, A and Banu, H and Majumdar, A and Chinnaswamy, S and Srinivasan, N and Dutta, S and Das, S (2020) Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. In: Journal of Biosciences, 45 (1).

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Abstract

Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2a clade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were also detected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein. Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz. G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutations reside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S2 domain, which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observed between these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations of miRNA binding and structure were also predicted for these mutations. More importantly, the possible implications of mutation D614G (in SD domain) and G1124V (in S2 subunit) on the structural stability of S protein have also been discussed. Results report for the first time a bird�s eye view on the accumulation of mutations in SARS-CoV-2 genome in Eastern India. © 2020, Indian Academy of Sciences.

Item Type:	Journal Article
Publication:	Journal of Biosciences
Publisher:	Springer
Additional Information:	Copy right for this article belongs to Springer
Keywords:	epidemiology; genome; mutation; protein; RNA; severe acute respiratory syndrome; viral disease, India, Miridae; SARS coronavirus, virus RNA, Betacoronavirus; Coronavirus infection; epidemic; genetics; human; India; mutation; pandemic; virology; virus pneumonia, Betacoronavirus; Coronavirus Infections; Disease Outbreaks; Host Microbial Interactions; Humans; India; Mutation; Pandemics; Pneumonia, Viral; RNA, Viral
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited:	25 Sep 2020 06:21
Last Modified:	25 Sep 2020 06:21
URI:	http://eprints.iisc.ac.in/id/eprint/65691

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